Quesneville H

References (18)

Title : The Rosa genome provides new insights into the domestication of modern roses - Raymond_2018_Nat.Genet_50_772
Author(s) : Raymond O , Gouzy J , Just J , Badouin H , Verdenaud M , Lemainque A , Vergne P , Moja S , Choisne N , Pont C , Carrere S , Caissard JC , Couloux A , Cottret L , Aury JM , Szecsi J , Latrasse D , Madoui MA , Francois L , Fu X , Yang SH , Dubois A , Piola F , Larrieu A , Perez M , Labadie K , Perrier L , Govetto B , Labrousse Y , Villand P , Bardoux C , Boltz V , Lopez-Roques C , Heitzler P , Vernoux T , Vandenbussche M , Quesneville H , Boualem A , Bendahmane A , Liu C , Le Bris M , Salse J , Baudino S , Benhamed M , Wincker P , Bendahmane M
Ref : Nat Genet , 50 :772 , 2018
Abstract : Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of 'La France', one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.
ESTHER : Raymond_2018_Nat.Genet_50_772
PubMedSearch : Raymond_2018_Nat.Genet_50_772
PubMedID: 29713014
Gene_locus related to this paper: rosch-a0a2p6p237 , rosch-a0a2p6r1h5 , rosch-a0a2p6saq0 , rosch-a0a2p6sap4 , rosch-a0a2p6san0 , rosch-a0a2p6san7 , rosch-a0a2p6rkg2 , rosch-a0a2p6pxu1 , rosch-a0a2p6s382 , rosch-a0a2p6s367 , rosch-a0a2p6q0b7 , rosch-a0a2p6pi87 , rosch-a0a2p6p278 , rosch-a0a2p6s545 , rosch-a0a2p6r6x5 , rosch-a0a2p6rqc2

Title : Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges - Gouin_2017_Sci.Rep_7_11816
Author(s) : Gouin A , Bretaudeau A , Nam K , Gimenez S , Aury JM , Duvic B , Hilliou F , Durand N , Montagne N , Darboux I , Kuwar S , Chertemps T , Siaussat D , Bretschneider A , Mone Y , Ahn SJ , Hanniger S , Grenet AG , Neunemann D , Maumus F , Luyten I , Labadie K , Xu W , Koutroumpa F , Escoubas JM , Llopis A , Mabeche-Coisne M , Salasc F , Tomar A , Anderson AR , Khan SA , Dumas P , Orsucci M , Guy J , Belser C , Alberti A , Noel B , Couloux A , Mercier J , Nidelet S , Dubois E , Liu NY , Boulogne I , Mirabeau O , Le Goff G , Gordon K , Oakeshott J , Consoli FL , Volkoff AN , Fescemyer HW , Marden JH , Luthe DS , Herrero S , Heckel DG , Wincker P , Kergoat GJ , Amselem J , Quesneville H , Groot AT , Jacquin-Joly E , Negre N , Lemaitre C , Legeai F , d'Alencon E , Fournier P
Ref : Sci Rep , 7 :11816 , 2017
Abstract : Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world's worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains ("C" and "R") that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
ESTHER : Gouin_2017_Sci.Rep_7_11816
PubMedSearch : Gouin_2017_Sci.Rep_7_11816
PubMedID: 28947760

Title : Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation - Willing_2015_Nat.Plants_1_14023
Author(s) : Willing EM , Rawat V , Mandakova T , Maumus F , James GV , Nordstrom KJ , Becker C , Warthmann N , Chica C , Szarzynska B , Zytnicki M , Albani MC , Kiefer C , Bergonzi S , Castaings L , Mateos JL , Berns MC , Bujdoso N , Piofczyk T , de Lorenzo L , Barrero-Sicilia C , Mateos I , Piednol M , Hagmann J , Chen-Min-Tao R , Iglesias-Fernandez R , Schuster SC , Alonso-Blanco C , Roudier F , Carbonero P , Paz-Ares J , Davis SJ , Pecinka A , Quesneville H , Colot V , Lysak MA , Weigel D , Coupland G , Schneeberger K
Ref : Nat Plants , 1 :14023 , 2015
Abstract : Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
ESTHER : Willing_2015_Nat.Plants_1_14023
PubMedSearch : Willing_2015_Nat.Plants_1_14023
PubMedID: 27246759
Gene_locus related to this paper: araal-a0a087gz21 , araal-a0a087h4k1

Title : Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus - Perlin_2015_BMC.Genomics_16_461
Author(s) : Perlin MH , Amselem J , Fontanillas E , Toh SS , Chen Z , Goldberg J , Duplessis S , Henrissat B , Young S , Zeng Q , Aguileta G , Petit E , Badouin H , Andrews J , Razeeq D , Gabaldon T , Quesneville H , Giraud T , Hood ME , Schultz DJ , Cuomo CA
Ref : BMC Genomics , 16 :461 , 2015
Abstract : BACKGROUND: The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. RESULTS: We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14% of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. CONCLUSIONS: The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.
ESTHER : Perlin_2015_BMC.Genomics_16_461
PubMedSearch : Perlin_2015_BMC.Genomics_16_461
PubMedID: 26076695
Gene_locus related to this paper: ustv1-u5h5e5

Title : Structural and functional partitioning of bread wheat chromosome 3B - Choulet_2014_Science_345_1249721
Author(s) : Choulet F , Alberti A , Theil S , Glover N , Barbe V , Daron J , Pingault L , Sourdille P , Couloux A , Paux E , Leroy P , Mangenot S , Guilhot N , Le Gouis J , Balfourier F , Alaux M , Jamilloux V , Poulain J , Durand C , Bellec A , Gaspin C , Safar J , Dolezel J , Rogers J , Vandepoele K , Aury JM , Mayer K , Berges H , Quesneville H , Wincker P , Feuillet C
Ref : Science , 345 :1249721 , 2014
Abstract : We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
ESTHER : Choulet_2014_Science_345_1249721
PubMedSearch : Choulet_2014_Science_345_1249721
PubMedID: 25035497
Gene_locus related to this paper: wheat-a0a080yuw6 , wheat-w5d1z6 , wheat-a0a077rex4 , wheat-a0a077s1q2

Title : The Capsella rubella genome and the genomic consequences of rapid mating system evolution - Slotte_2013_Nat.Genet_45_831
Author(s) : Slotte T , Hazzouri KM , Agren JA , Koenig D , Maumus F , Guo YL , Steige K , Platts AE , Escobar JS , Newman LK , Wang W , Mandakova T , Vello E , Smith LM , Henz SR , Steffen J , Takuno S , Brandvain Y , Coop G , Andolfatto P , Hu TT , Blanchette M , Clark RM , Quesneville H , Nordborg M , Gaut BS , Lysak MA , Jenkins J , Grimwood J , Chapman J , Prochnik S , Shu S , Rokhsar D , Schmutz J , Weigel D , Wright SI
Ref : Nat Genet , 45 :831 , 2013
Abstract : The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
ESTHER : Slotte_2013_Nat.Genet_45_831
PubMedSearch : Slotte_2013_Nat.Genet_45_831
PubMedID: 23749190
Gene_locus related to this paper: arath-CGEP , 9bras-r0h1k6 , 9bras-r0gvg3 , 9bras-r0gv62 , 9bras-r0g5k5 , 9bras-r0f1u1 , 9bras-r0guy4 , 9bras-r0ien7 , 9bras-r0i2r7 , 9bras-r0fbh7 , 9bras-r0fnq1 , 9bras-r0hae6 , 9bras-r0gwt8 , 9bras-r0ewe4 , 9bras-r0gsz7 , 9bras-r0ij26 , 9bras-r0h783 , 9bras-r0i5w1 , 9bras-r0fgs3 , 9bras-r0h1e1 , 9bras-r0fme4 , 9bras-r0ieh8 , 9bras-r0f5l9 , 9bras-r0ffy6

Title : Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations - Rouxel_2011_Nat.Commun_2_202
Author(s) : Rouxel T , Grandaubert J , Hane JK , Hoede C , van de Wouw AP , Couloux A , Dominguez V , Anthouard V , Bally P , Bourras S , Cozijnsen AJ , Ciuffetti LM , Degrave A , Dilmaghani A , Duret L , Fudal I , Goodwin SB , Gout L , Glaser N , Linglin J , Kema GH , Lapalu N , Lawrence CB , May K , Meyer M , Ollivier B , Poulain J , Schoch CL , Simon A , Spatafora JW , Stachowiak A , Turgeon BG , Tyler BM , Vincent D , Weissenbach J , Amselem J , Quesneville H , Oliver RP , Wincker P , Balesdent MH , Howlett BJ
Ref : Nat Commun , 2 :202 , 2011
Abstract : Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
ESTHER : Rouxel_2011_Nat.Commun_2_202
PubMedSearch : Rouxel_2011_Nat.Commun_2_202
PubMedID: 21326234
Gene_locus related to this paper: lepmc-q6q891 , lepmj-e4zh04 , lepmj-e4ziv6 , lepmj-e4zju4 , lepmj-e4zqu4 , lepmj-e4zvh3 , lepmj-e4zvl4 , lepmj-e4zx66 , lepmj-e5a0i2 , lepmj-e5a510 , lepmj-e5aau5 , lepmj-e5acd1 , lepmj-e5a4g5 , lepmj-e4zhg2 , lepmj-e4zuw5 , lepmj-e5a2e0 , lepmj-e4zpv2 , lepmj-e4zxp4 , lepmj-e4zpy5 , lepmj-e5ae17 , lepmj-e4ziv2 , lepmj-e5a374 , lepmj-e5ab81 , lepmj-e4zgy1 , lepmj-e4zg43 , lepmj-kex1 , lepmj-cbpya

Title : Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea - Amselem_2011_PLoS.Genet_7_e1002230
Author(s) : Amselem J , Cuomo CA , van Kan JA , Viaud M , Benito EP , Couloux A , Coutinho PM , de Vries RP , Dyer PS , Fillinger S , Fournier E , Gout L , Hahn M , Kohn L , Lapalu N , Plummer KM , Pradier JM , Quevillon E , Sharon A , Simon A , ten Have A , Tudzynski B , Tudzynski P , Wincker P , Andrew M , Anthouard V , Beever RE , Beffa R , Benoit I , Bouzid O , Brault B , Chen Z , Choquer M , Collemare J , Cotton P , Danchin EG , Da Silva C , Gautier A , Giraud C , Giraud T , Gonzalez C , Grossetete S , Guldener U , Henrissat B , Howlett BJ , Kodira C , Kretschmer M , Lappartient A , Leroch M , Levis C , Mauceli E , Neuveglise C , Oeser B , Pearson M , Poulain J , Poussereau N , Quesneville H , Rascle C , Schumacher J , Segurens B , Sexton A , Silva E , Sirven C , Soanes DM , Talbot NJ , Templeton M , Yandava C , Yarden O , Zeng Q , Rollins JA , Lebrun MH , Dickman M
Ref : PLoS Genet , 7 :e1002230 , 2011
Abstract : Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
ESTHER : Amselem_2011_PLoS.Genet_7_e1002230
PubMedSearch : Amselem_2011_PLoS.Genet_7_e1002230
PubMedID: 21876677
Gene_locus related to this paper: botci-cutas , botci-q6rki2 , botf4-g2y7k8 , botfb-dapb , botfu-g2xyd8 , botfu-g2ynh8 , scls1-a7e814 , scls1-a7edc9 , scls1-a7edh1 , scls1-a7emm0 , scls1-a7eti8 , scls1-a7eu48 , scls1-a7f208 , scls1-dapb , botf4-g2xqp7 , scls1-a7eqq8 , botf4-g2xqc6 , scls1-a7ebs4 , botf4-g2xn51 , scls1-a7f5m9 , botf4-g2xti4 , botf4-g2xtu7 , botf4-g2yfp1 , scls1-a7f534 , botf4-g2yys3 , scls1-a7erz9 , botf4-g2y037 , botf4-g2y0e1 , scls1-a7f706 , scls1-a7ewt6 , botf4-g2yuj6 , botf1-m7u3d1 , botf1-m7u430 , botf1-m7tei8 , botf1-m7u0w9 , botf1-m7tij6 , botf1-m7u819 , botf1-m7u6d8 , botf1-m7tzd4 , botf1-m7tqd7 , botf1-m7tyz9 , botf1-m7unl9 , botf1-m7u429 , botf1-m7u4s5 , botf1-m7ul92 , botf1-m7tx42 , botf1-m7u9h4 , botf1-m7u187 , botf1-m7uz64 , botf1-m7u4q4 , botf1-m7u2f6 , botf1-m7tt59 , botf1-m7v3h2 , botf1-m7u6c9 , botf1-m7tud9 , botf1-m7u309 , scls1-a7et87 , botf4-g2ylt4 , scls1-a7f5a0 , scls1-a7f900 , botf4-g2yib9 , scls1-a7f3m9 , scls1-a7er46 , botf4-g2y3y4 , botf4-g2xyy5 , botf1-m7uct5 , scls1-a7ea78 , scls1-kex1 , scls1-cbpya , botfb-cbpya , scls1-a7ecx1

Title : Obligate biotrophy features unraveled by the genomic analysis of rust fungi - Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
Author(s) : Duplessis S , Cuomo CA , Lin YC , Aerts A , Tisserant E , Veneault-Fourrey C , Joly DL , Hacquard S , Amselem J , Cantarel BL , Chiu R , Coutinho PM , Feau N , Field M , Frey P , Gelhaye E , Goldberg J , Grabherr MG , Kodira CD , Kohler A , Kues U , Lindquist EA , Lucas SM , Mago R , Mauceli E , Morin E , Murat C , Pangilinan JL , Park R , Pearson M , Quesneville H , Rouhier N , Sakthikumar S , Salamov AA , Schmutz J , Selles B , Shapiro H , Tanguay P , Tuskan GA , Henrissat B , Van de Peer Y , Rouze P , Ellis JG , Dodds PN , Schein JE , Zhong S , Hamelin RC , Grigoriev IV , Szabo LJ , Martin F
Ref : Proc Natl Acad Sci U S A , 108 :9166 , 2011
Abstract : Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
ESTHER : Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedSearch : Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedID: 21536894
Gene_locus related to this paper: pucgt-e3k840 , pucgt-e3kaq6 , pucgt-e3kw59 , pucgt-e3kz16 , pucgt-e3l9v6 , pucgt-e3l279 , pucgt-h6qt25 , mellp-f4reh4 , mellp-f4rhc8 , mellp-f4reh2 , mellp-f4r3y0 , mellp-f4rz15 , mellp-f4rz64 , mellp-f4rl14 , mellp-f4rz66 , mellp-f4s751 , mellp-f4s2g6 , pucgt-e3l1z7 , pucgt-e3l803 , pucgt-e3kst2 , pucgt-e3kst5 , mellp-f4ru03 , pucgt-e3l1z8 , pucgt-e3ktz7 , pucgt-e3jun4 , mellp-f4rl65 , mellp-f4rz16 , mellp-f4ru02 , mellp-f4sav4 , mellp-f4sav3 , mellp-f4s1j0 , mellp-f4rkp0 , mellp-f4s483 , pucgt-e3kzu5 , pucgt-h6qtq8 , mellp-f4r5l5 , pucgt-e3krw7 , pucgt-e3l7w5 , pucgt-e3k2w6 , pucgt-e3kfg2 , pucgt-kex1

Title : Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism - Spanu_2010_Science_330_1543
Author(s) : Spanu PD , Abbott JC , Amselem J , Burgis TA , Soanes DM , Stuber K , Ver Loren van Themaat E , Brown JK , Butcher SA , Gurr SJ , Lebrun MH , Ridout CJ , Schulze-Lefert P , Talbot NJ , Ahmadinejad N , Ametz C , Barton GR , Benjdia M , Bidzinski P , Bindschedler LV , Both M , Brewer MT , Cadle-Davidson L , Cadle-Davidson MM , Collemare J , Cramer R , Frenkel O , Godfrey D , Harriman J , Hoede C , King BC , Klages S , Kleemann J , Knoll D , Koti PS , Kreplak J , Lopez-Ruiz FJ , Lu X , Maekawa T , Mahanil S , Micali C , Milgroom MG , Montana G , Noir S , O'Connell RJ , Oberhaensli S , Parlange F , Pedersen C , Quesneville H , Reinhardt R , Rott M , Sacristan S , Schmidt SM , Schon M , Skamnioti P , Sommer H , Stephens A , Takahara H , Thordal-Christensen H , Vigouroux M , Wessling R , Wicker T , Panstruga R
Ref : Science , 330 :1543 , 2010
Abstract : Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
ESTHER : Spanu_2010_Science_330_1543
PubMedSearch : Spanu_2010_Science_330_1543
PubMedID: 21148392
Gene_locus related to this paper: blugr-d2cql4 , blug1-n1jlh9 , blug1-n1j5n4 , blug1-n1j9r9 , blug1-n1je34 , blug1-n1jkm5 , blug1-n1jhv6 , blug1-n1j8l0 , blug1-n1jqj7 , blug1-n1j543

Title : Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis - Martin_2010_Nature_464_1033
Author(s) : Martin F , Kohler A , Murat C , Balestrini R , Coutinho PM , Jaillon O , Montanini B , Morin E , Noel B , Percudani R , Porcel B , Rubini A , Amicucci A , Amselem J , Anthouard V , Arcioni S , Artiguenave F , Aury JM , Ballario P , Bolchi A , Brenna A , Brun A , Buee M , Cantarel B , Chevalier G , Couloux A , Da Silva C , Denoeud F , Duplessis S , Ghignone S , Hilselberger B , Iotti M , Marcais B , Mello A , Miranda M , Pacioni G , Quesneville H , Riccioni C , Ruotolo R , Splivallo R , Stocchi V , Tisserant E , Viscomi AR , Zambonelli A , Zampieri E , Henrissat B , Lebrun MH , Paolocci F , Bonfante P , Ottonello S , Wincker P
Ref : Nature , 464 :1033 , 2010
Abstract : The Perigord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.
ESTHER : Martin_2010_Nature_464_1033
PubMedSearch : Martin_2010_Nature_464_1033
PubMedID: 20348908
Gene_locus related to this paper: 9pezi-d5g8f4 , 9pezi-d5gi84 , 9pezi-d5gph4 , tubmm-d5g4w2 , tubmm-d5g4w3 , tubmm-d5g4w6 , tubmm-d5g5r5 , tubmm-d5g8z4 , tubmm-d5g938 , tubmm-d5ga65 , tubmm-d5gcz1 , tubmm-d5giz0 , tubmm-d5gkr8 , tubmm-d5glm4 , tubmm-d5gnw0 , tubmm-dapb , tubmm-d5gfj1 , tubmm-d5gpf4 , tubmm-TmEst2 , tubmm-TmEst1 , tubmm-TmEst3 , 9pezi-a0a292py12 , tubmm-kex1

Title : The Ectocarpus genome and the independent evolution of multicellularity in brown algae - Cock_2010_Nature_465_617
Author(s) : Cock JM , Sterck L , Rouze P , Scornet D , Allen AE , Amoutzias G , Anthouard V , Artiguenave F , Aury JM , Badger JH , Beszteri B , Billiau K , Bonnet E , Bothwell JH , Bowler C , Boyen C , Brownlee C , Carrano CJ , Charrier B , Cho GY , Coelho SM , Collen J , Corre E , Da Silva C , Delage L , Delaroque N , Dittami SM , Doulbeau S , Elias M , Farnham G , Gachon CM , Gschloessl B , Heesch S , Jabbari K , Jubin C , Kawai H , Kimura K , Kloareg B , Kupper FC , Lang D , Le Bail A , LeBlanc C , Lerouge P , Lohr M , Lopez PJ , Martens C , Maumus F , Michel G , Miranda-Saavedra D , Morales J , Moreau H , Motomura T , Nagasato C , Napoli CA , Nelson DR , Nyvall-Collen P , Peters AF , Pommier C , Potin P , Poulain J , Quesneville H , Read B , Rensing SA , Ritter A , Rousvoal S , Samanta M , Samson G , Schroeder DC , Segurens B , Strittmatter M , Tonon T , Tregear JW , Valentin K , von Dassow P , Yamagishi T , Van de Peer Y , Wincker P
Ref : Nature , 465 :617 , 2010
Abstract : Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
ESTHER : Cock_2010_Nature_465_617
PubMedSearch : Cock_2010_Nature_465_617
PubMedID: 20520714
Gene_locus related to this paper: ectsi-d7fm61 , ectsi-d7fs16 , ectsi-d7fsv3 , ectsi-d7fte8 , ectsi-d7fux6 , ectsi-d7fvr0 , ectsi-d7fvu4 , ectsi-d7fwk0 , ectsi-d7fyh7 , ectsi-d7g0w7 , ectsi-d7g6g5 , ectsi-d7g484 , ectsi-d7g686 , ectsi-d8lca9 , ectsi-d8lfv2 , ectsi-d8lqg6 , ectsi-d8ltj9 , ectsi-d7fjz2 , ectsi-d7g376

Title : The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis - Martin_2008_Nature_452_88
Author(s) : Martin F , Aerts A , Ahren D , Brun A , Danchin EG , Duchaussoy F , Gibon J , Kohler A , Lindquist E , Pereda V , Salamov A , Shapiro HJ , Wuyts J , Blaudez D , Buee M , Brokstein P , Canback B , Cohen D , Courty PE , Coutinho PM , Delaruelle C , Detter JC , Deveau A , Difazio S , Duplessis S , Fraissinet-Tachet L , Lucic E , Frey-Klett P , Fourrey C , Feussner I , Gay G , Grimwood J , Hoegger PJ , Jain P , Kilaru S , Labbe J , Lin YC , Legue V , Le Tacon F , Marmeisse R , Melayah D , Montanini B , Muratet M , Nehls U , Niculita-Hirzel H , Oudot-Le Secq MP , Peter M , Quesneville H , Rajashekar B , Reich M , Rouhier N , Schmutz J , Yin T , Chalot M , Henrissat B , Kues U , Lucas S , Van de Peer Y , Podila GK , Polle A , Pukkila PJ , Richardson PM , Rouze P , Sanders IR , Stajich JE , Tunlid A , Tuskan G , Grigoriev IV
Ref : Nature , 452 :88 , 2008
Abstract : Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
ESTHER : Martin_2008_Nature_452_88
PubMedSearch : Martin_2008_Nature_452_88
PubMedID: 18322534
Gene_locus related to this paper: lacbs-b0cns1 , lacbs-b0cpl4 , lacbs-b0cr62 , lacbs-b0cr66 , lacbs-b0csq9 , lacbs-b0ct56 , lacbs-b0ctt5 , lacbs-b0cuw1 , lacbs-b0cv23 , lacbs-b0cxm7 , lacbs-b0cz37 , lacbs-b0czx3 , lacbs-b0d0z5 , lacbs-b0d4i0 , lacbs-b0d4j3 , lacbs-b0d5n6 , lacbs-b0d8k0 , lacbs-b0d263 , lacbs-b0dhh1 , lacbs-b0dkp6 , lacbs-b0dmr2 , lacbs-b0dmt4 , lacbs-b0dsx5 , lacbs-b0dt05 , lacbs-b0dtw4 , lacbs-b0du88 , lacbs-b0dsl6

Title : Evolution of genes and genomes on the Drosophila phylogeny - Clark_2007_Nature_450_203
Author(s) : Clark AG , Eisen MB , Smith DR , Bergman CM , Oliver B , Markow TA , Kaufman TC , Kellis M , Gelbart W , Iyer VN , Pollard DA , Sackton TB , Larracuente AM , Singh ND , Abad JP , Abt DN , Adryan B , Aguade M , Akashi H , Anderson WW , Aquadro CF , Ardell DH , Arguello R , Artieri CG , Barbash DA , Barker D , Barsanti P , Batterham P , Batzoglou S , Begun D , Bhutkar A , Blanco E , Bosak SA , Bradley RK , Brand AD , Brent MR , Brooks AN , Brown RH , Butlin RK , Caggese C , Calvi BR , Bernardo de Carvalho A , Caspi A , Castrezana S , Celniker SE , Chang JL , Chapple C , Chatterji S , Chinwalla A , Civetta A , Clifton SW , Comeron JM , Costello JC , Coyne JA , Daub J , David RG , Delcher AL , Delehaunty K , Do CB , Ebling H , Edwards K , Eickbush T , Evans JD , Filipski A , Findeiss S , Freyhult E , Fulton L , Fulton R , Garcia AC , Gardiner A , Garfield DA , Garvin BE , Gibson G , Gilbert D , Gnerre S , Godfrey J , Good R , Gotea V , Gravely B , Greenberg AJ , Griffiths-Jones S , Gross S , Guigo R , Gustafson EA , Haerty W , Hahn MW , Halligan DL , Halpern AL , Halter GM , Han MV , Heger A , Hillier L , Hinrichs AS , Holmes I , Hoskins RA , Hubisz MJ , Hultmark D , Huntley MA , Jaffe DB , Jagadeeshan S , Jeck WR , Johnson J , Jones CD , Jordan WC , Karpen GH , Kataoka E , Keightley PD , Kheradpour P , Kirkness EF , Koerich LB , Kristiansen K , Kudrna D , Kulathinal RJ , Kumar S , Kwok R , Lander E , Langley CH , Lapoint R , Lazzaro BP , Lee SJ , Levesque L , Li R , Lin CF , Lin MF , Lindblad-Toh K , Llopart A , Long M , Low L , Lozovsky E , Lu J , Luo M , Machado CA , Makalowski W , Marzo M , Matsuda M , Matzkin L , McAllister B , McBride CS , McKernan B , McKernan K , Mendez-Lago M , Minx P , Mollenhauer MU , Montooth K , Mount SM , Mu X , Myers E , Negre B , Newfeld S , Nielsen R , Noor MA , O'Grady P , Pachter L , Papaceit M , Parisi MJ , Parisi M , Parts L , Pedersen JS , Pesole G , Phillippy AM , Ponting CP , Pop M , Porcelli D , Powell JR , Prohaska S , Pruitt K , Puig M , Quesneville H , Ram KR , Rand D , Rasmussen MD , Reed LK , Reenan R , Reily A , Remington KA , Rieger TT , Ritchie MG , Robin C , Rogers YH , Rohde C , Rozas J , Rubenfield MJ , Ruiz A , Russo S , Salzberg SL , Sanchez-Gracia A , Saranga DJ , Sato H , Schaeffer SW , Schatz MC , Schlenke T , Schwartz R , Segarra C , Singh RS , Sirot L , Sirota M , Sisneros NB , Smith CD , Smith TF , Spieth J , Stage DE , Stark A , Stephan W , Strausberg RL , Strempel S , Sturgill D , Sutton G , Sutton GG , Tao W , Teichmann S , Tobari YN , Tomimura Y , Tsolas JM , Valente VL , Venter E , Venter JC , Vicario S , Vieira FG , Vilella AJ , Villasante A , Walenz B , Wang J , Wasserman M , Watts T , Wilson D , Wilson RK , Wing RA , Wolfner MF , Wong A , Wong GK , Wu CI , Wu G , Yamamoto D , Yang HP , Yang SP , Yorke JA , Yoshida K , Zdobnov E , Zhang P , Zhang Y , Zimin AV , Baldwin J , Abdouelleil A , Abdulkadir J , Abebe A , Abera B , Abreu J , Acer SC , Aftuck L , Alexander A , An P , Anderson E , Anderson S , Arachi H , Azer M , Bachantsang P , Barry A , Bayul T , Berlin A , Bessette D , Bloom T , Blye J , Boguslavskiy L , Bonnet C , Boukhgalter B , Bourzgui I , Brown A , Cahill P , Channer S , Cheshatsang Y , Chuda L , Citroen M , Collymore A , Cooke P , Costello M , D'Aco K , Daza R , De Haan G , DeGray S , DeMaso C , Dhargay N , Dooley K , Dooley E , Doricent M , Dorje P , Dorjee K , Dupes A , Elong R , Falk J , Farina A , Faro S , Ferguson D , Fisher S , Foley CD , Franke A , Friedrich D , Gadbois L , Gearin G , Gearin CR , Giannoukos G , Goode T , Graham J , Grandbois E , Grewal S , Gyaltsen K , Hafez N , Hagos B , Hall J , Henson C , Hollinger A , Honan T , Huard MD , Hughes L , Hurhula B , Husby ME , Kamat A , Kanga B , Kashin S , Khazanovich D , Kisner P , Lance K , Lara M , Lee W , Lennon N , Letendre F , LeVine R , Lipovsky A , Liu X , Liu J , Liu S , Lokyitsang T , Lokyitsang Y , Lubonja R , Lui A , Macdonald P , Magnisalis V , Maru K , Matthews C , McCusker W , McDonough S , Mehta T , Meldrim J , Meneus L , Mihai O , Mihalev A , Mihova T , Mittelman R , Mlenga V , Montmayeur A , Mulrain L , Navidi A , Naylor J , Negash T , Nguyen T , Nguyen N , Nicol R , Norbu C , Norbu N , Novod N , O'Neill B , Osman S , Markiewicz E , Oyono OL , Patti C , Phunkhang P , Pierre F , Priest M , Raghuraman S , Rege F , Reyes R , Rise C , Rogov P , Ross K , Ryan E , Settipalli S , Shea T , Sherpa N , Shi L , Shih D , Sparrow T , Spaulding J , Stalker J , Stange-Thomann N , Stavropoulos S , Stone C , Strader C , Tesfaye S , Thomson T , Thoulutsang Y , Thoulutsang D , Topham K , Topping I , Tsamla T , Vassiliev H , Vo A , Wangchuk T , Wangdi T , Weiand M , Wilkinson J , Wilson A , Yadav S , Young G , Yu Q , Zembek L , Zhong D , Zimmer A , Zwirko Z , Alvarez P , Brockman W , Butler J , Chin C , Grabherr M , Kleber M , Mauceli E , MacCallum I
Ref : Nature , 450 :203 , 2007
Abstract : Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
ESTHER : Clark_2007_Nature_450_203
PubMedSearch : Clark_2007_Nature_450_203
PubMedID: 17994087
Gene_locus related to this paper: droan-ACHE , droan-b3lx10 , droan-b3lx75 , droan-b3lxv7 , droan-b3ly87 , droan-b3lyh4 , droan-b3lyh5 , droan-b3lyh7 , droan-b3lyh9 , droan-b3lyi0 , droan-b3lyi2 , droan-b3lyi3 , droan-b3lyi4 , droan-b3lyj8 , droan-b3lyj9 , droan-b3lyx4 , droan-b3lyx5 , droan-b3lyx6 , droan-b3lyx7 , droan-b3lyx9 , droan-b3lz72 , droan-b3m1x3 , droan-b3m2d4 , droan-b3m3d9 , droan-b3m4e3 , droan-b3m5w1 , droan-b3m6i7 , droan-b3m7v2 , droan-b3m9a5 , droan-b3m9f4 , droan-b3m9p3 , droan-b3m254 , droan-b3m259 , droan-b3m260 , droan-b3m262 , droan-b3m524 , droan-b3m635 , droan-b3m845 , droan-b3m846 , droan-b3md01 , droan-b3mdh7 , droan-b3mdm6 , droan-b3mdw8 , droan-b3mee1 , droan-b3mf47 , droan-b3mf48 , droan-b3mg94 , droan-b3mgk2 , droan-b3mgn6 , droan-b3mii3 , droan-b3mjk2 , droan-b3mjk3 , droan-b3mjk4 , droan-b3mjk5 , droan-b3mjl2 , droan-b3mjl4 , droan-b3mjl7 , droan-b3mjl9 , droan-b3mjm8 , droan-b3mjm9 , droan-b3mjs6 , droan-b3mkr0 , droan-b3ml20 , droan-b3mly4 , droan-b3mly5 , droan-b3mly6 , droan-b3mmm8 , droan-b3mnb5 , droan-b3mny9 , droan-b3mtj5 , droan-b3muw4 , droan-b3muw8 , droan-b3n0e7 , droan-b3n2j7 , droan-b3n247 , droan-c5idb2 , droer-ACHE , droer-b3n5c7 , droer-b3n5d0 , droer-b3n5d8 , droer-b3n5d9 , droer-b3n5t7 , droer-b3n5y4 , droer-b3n7d2 , droer-b3n7d3 , droer-b3n7d4 , droer-b3n7k8 , droer-b3n8e4 , droer-b3n8f7 , droer-b3n8f8 , droer-b3n9e1 , droer-b3n319 , droer-b3n547 , droer-b3n549 , droer-b3n558 , droer-b3n560 , droer-b3n577 , droer-b3n612 , droer-b3nar5 , droer-b3nb91 , droer-b3nct9 , droer-b3nd53 , droer-b3ndh9 , droer-b3ndq8 , droer-b3ne66 , droer-b3ne67 , droer-b3ne97 , droer-b3nfk3 , droer-b3nfq9 , droer-b3nim7 , droer-b3nkn2 , droer-b3nm11 , droer-b3nmh4 , droer-b3nmy2 , droer-b3npx2 , droer-b3npx3 , droer-b3nq76 , droer-b3nqg9 , droer-b3nqm8 , droer-b3nr28 , droer-b3nrd3 , droer-b3nst4 , droer-b3nwa7 , droer-b3nyp5.1 , droer-b3nyp5.2 , droer-b3nyp6 , droer-b3nyp7 , droer-b3nyp8 , droer-b3nyp9 , droer-b3nyq3 , droer-b3nz06 , droer-b3nz14 , droer-b3nzj0 , droer-b3p0c0 , droer-b3p0c1 , droer-b3p0c2 , droer-b3p2x6 , droer-b3p2x7 , droer-b3p2x9 , droer-b3p2y1 , droer-b3p2y2 , droer-b3p6d4 , droer-b3p6d5 , droer-b3p6w3 , droer-b3p7b4 , droer-b3p7h9 , droer-b3p152 , droer-b3p486 , droer-b3p487 , droer-b3p488 , droer-b3p489 , droer-EST6 , droer-q670j5 , drogr-ACHE , drogr-b4iwp3 , drogr-b4iww3 , drogr-b4iwy3 , drogr-b4ixf7 , drogr-b4ixh4 , drogr-b4iyz5 , drogr-b4j2s2 , drogr-b4j2u8 , drogr-b4j3u1 , drogr-b4j3v3 , drogr-b4j4g7 , drogr-b4j4x9 , drogr-b4j6e6 , drogr-b4j9c9 , drogr-b4j9y4 , drogr-b4j156 , drogr-b4j384 , drogr-b4j605 , drogr-b4j685 , drogr-b4ja76 , drogr-b4jay5 , drogr-b4jcf0 , drogr-b4jcf1 , drogr-b4jdg6 , drogr-b4jdg7 , drogr-b4jdh6 , drogr-b4jdz1 , drogr-b4jdz2 , drogr-b4jdz4 , drogr-b4je66 , drogr-b4je79 , drogr-b4je82 , drogr-b4je88 , drogr-b4je89 , drogr-b4je90 , drogr-b4je91 , drogr-b4jf76 , drogr-b4jf79 , drogr-b4jf80 , drogr-b4jf81 , drogr-b4jf82 , drogr-b4jf83 , drogr-b4jf84 , drogr-b4jf85 , drogr-b4jf87 , drogr-b4jf91 , drogr-b4jf92 , drogr-b4jg66 , drogr-b4jgh0 , drogr-b4jgh1 , drogr-b4jgr9 , drogr-b4ji67 , drogr-b4jls2 , drogr-b4jnh9 , drogr-b4jpc6 , drogr-b4jpq3 , drogr-b4jpx9 , drogr-b4jql2 , drogr-b4jrh5 , drogr-b4jsb2 , drogr-b4jth3 , drogr-b4jti1 , drogr-b4jul5 , drogr-b4jur4 , drogr-b4jvh3 , drogr-b4jz00 , drogr-b4jz03 , drogr-b4jz04 , drogr-b4jz05 , drogr-b4jzh2 , drogr-b4k0u2 , drogr-b4k2r1 , drogr-b4k234 , drogr-b4k235 , drome-BEM46 , drome-CG3734 , drome-CG9953 , drome-CG11626 , drome-GH02439 , dromo-ACHE , dromo-b4k6a7 , dromo-b4k6a8 , dromo-b4k6q8 , dromo-b4k6q9 , dromo-b4k6r1 , dromo-b4k6r3 , dromo-b4k6r4 , dromo-b4k6r5 , dromo-b4k6r6 , dromo-b4k6r7 , dromo-b4k6r8 , dromo-b4k6r9 , dromo-b4k6s0 , dromo-b4k6s1 , dromo-b4k6s2 , dromo-b4k9c7 , dromo-b4k9d3 , dromo-b4k571 , dromo-b4k721 , dromo-b4ka74 , dromo-b4ka89 , dromo-b4kaj4 , dromo-b4kc20 , dromo-b4kcl2 , dromo-b4kcl3 , dromo-b4kd55.1 , dromo-b4kd55.2 , dromo-b4kd56 , dromo-b4kd57 , dromo-b4kde1 , dromo-b4kdg2 , dromo-b4kdh4 , dromo-b4kdh5 , dromo-b4kdh6 , dromo-A0A0Q9XDF2 , dromo-b4kdh8.1 , dromo-b4kdh8.2 , dromo-b4kg04 , dromo-b4kg05 , dromo-b4kg06 , dromo-b4kg16 , dromo-b4kg44 , dromo-b4kg90 , dromo-b4kh20 , dromo-b4kh21 , dromo-b4kht7 , dromo-b4kid3 , dromo-b4kik0 , dromo-b4kjx0 , dromo-b4kki1 , dromo-b4kkp6 , dromo-b4kkp8 , dromo-b4kkq8 , dromo-b4kkr0 , dromo-b4kkr3 , dromo-b4kkr4 , dromo-b4kks0 , dromo-b4kks1 , dromo-b4kks2 , dromo-b4kla1 , dromo-b4klv8 , dromo-b4knt4 , dromo-b4kp08 , dromo-b4kp16 , dromo-b4kqa6 , dromo-b4kqa7 , dromo-b4kqa8 , dromo-b4kqh1 , dromo-b4kst4 , dromo-b4ksy6 , dromo-b4kt84 , dromo-b4ktf5 , dromo-b4ktf6 , dromo-b4kvl3 , dromo-b4kvw2 , dromo-b4kwv4 , dromo-b4kwv5 , dromo-b4kxz6 , dromo-b4ky12 , dromo-b4ky36 , dromo-b4ky44 , dromo-b4kzu7 , dromo-b4l0n8 , dromo-b4l4u5 , dromo-b4l6l9 , dromo-b4l084 , drope-ACHE , drope-b4g3s6 , drope-b4g4p7 , drope-b4g6v4 , drope-b4g8m0 , drope-b4g8n6 , drope-b4g8n7 , drope-b4g9p2 , drope-b4g815 , drope-b4g816 , drope-b4gat7 , drope-b4gav5 , drope-b4gb05 , drope-b4gc08 , drope-b4gcr3 , drope-b4gdk2 , drope-b4gdl9 , drope-b4gdv9 , drope-b4gei8 , drope-b4gei9 , drope-b4gej0 , drope-b4ghz9 , drope-b4gj62 , drope-b4gj64 , drope-b4gj74 , drope-b4gkf4 , drope-b4gkv2 , drope-b4gky9 , drope-b4gl76 , drope-b4glf3 , drope-b4gmt3 , drope-b4gmt7 , drope-b4gmt9 , drope-b4gmu2 , drope-b4gmu3 , drope-b4gmu4 , drope-b4gmu5 , drope-b4gmu6 , drope-b4gmu7 , drope-b4gmv1 , drope-b4gn08 , drope-b4gpa7 , drope-b4gq13 , drope-b4grh7 , drope-b4gsf9 , drope-b4gsw4 , drope-b4gsw5 , drope-b4gsx2 , drope-b4gsx7 , drope-b4gsy6 , drope-b4gsy7 , drope-b4guj8 , drope-b4gw36 , drope-b4gzc2 , drope-b4gzc6 , drope-b4gzc7 , drope-b4h4p9 , drope-b4h5l3 , drope-b4h6a0 , drope-b4h6a8 , drope-b4h6a9 , drope-b4h6b0 , drope-b4h7m7 , drope-b4h462 , drope-b4h601 , drope-b4h602 , drope-b4hay1 , drope-b4hb18 , drope-est5a , drope-est5b , drope-est5c , drops-ACHE , drops-b5dhd2 , drops-b5dk96 , drops-b5dpe3 , drops-b5drp9 , drops-b5dwa7 , drops-b5dwa8 , drops-b5dz85 , drops-b5dz86 , drops-est5a , drops-est5b , drops-q29bq2 , drops-q29dd7 , drops-q29ew0 , drops-q291d5 , drops-q291e8 , drops-q293n1 , drops-q293n4 , drops-q293n5 , drops-q293n6 , drops-q294n6 , drops-q294n7 , drops-q294n9 , drops-q294p4 , drose-b4he97 , drose-b4hfu2 , drose-b4hg54 , drose-b4hga0 , drose-b4hgu9 , drose-b4hgv0 , drose-b4hgv3 , drose-b4hgv4 , drose-b4hhm8 , drose-b4hhs6 , drose-b4hie4 , drose-b4him9 , drose-b4hk63 , drose-b4hkj5 , drose-b4hr07 , drose-b4hr81 , drose-b4hre7 , drose-b4hs13 , drose-b4hsj9 , drose-b4hsk0 , drose-b4hsm8 , drose-b4hvr5 , drose-b4hwr7 , drose-b4hwr8 , drose-b4hwr9 , drose-b4hws6 , drose-b4hws7 , drose-b4hwt0 , drose-b4hwt2 , drose-b4hwu1 , drose-b4hwu2 , drose-b4hxs9 , drose-b4hxu4 , drose-b4hxz1 , drose-b4hyp8 , drose-b4hyp9 , drose-b4hyq0 , drose-b4hyz4 , drose-b4hyz5 , drose-b4i1k8 , drose-b4i2f3 , drose-b4i2w5 , drose-b4i4u3 , drose-b4i4u7 , drose-b4i4u9 , drose-b4i4v0 , drose-b4i4v1 , drose-b4i4v4 , drose-b4i4v5 , drose-b4i4v6 , drose-b4i4v7 , drose-b4i4v8 , drose-b4i4w0 , drose-b4i7s6 , drose-b4i133 , drose-b4i857 , drose-b4iam7 , drose-b4iam9 , drose-b4iaq6 , drose-b4icf6 , drose-b4icf7 , drose-b4id80 , drose-b4ifc5 , drose-b4ihv9 , drose-b4iie9 , drose-b4ilj8 , drose-b4in13 , drose-b4inj9 , drosi-ACHE , drosi-aes04a , drosi-b4nsh8 , drosi-b4q3d7 , drosi-b4q4w5 , drosi-b4q4y7 , drosi-b4q6h6 , drosi-b4q7u2 , drosi-b4q7u3 , drosi-b4q9c6 , drosi-b4q9c7 , drosi-b4q9d3 , drosi-b4q9d4 , drosi-b4q9r0 , drosi-b4q9r1 , drosi-b4q9r3 , drosi-b4q9s2 , drosi-b4q9s3 , drosi-b4q429 , drosi-b4q530 , drosi-b4q734 , drosi-b4q782 , drosi-b4q783 , drosi-b4q942 , drosi-b4qet1 , drosi-b4qfv6 , drosi-b4qge5 , drosi-b4qgh5 , drosi-b4qgs5 , drosi-b4qhf3 , drosi-b4qhf4 , drosi-b4qhi5 , drosi-b4qjr2 , drosi-b4qjr3 , drosi-b4qjv6 , drosi-b4qk23 , drosi-b4qk51 , drosi-b4qlt1 , drosi-b4qlz9 , drosi-b4qmn9 , drosi-b4qrq7 , drosi-b4qs01 , drosi-b4qs57 , drosi-b4qs82 , drosi-b4qs83 , drosi-b4qs84 , drosi-b4qs85 , drosi-b4qs86 , drosi-b4qsq1 , drosi-b4quk6 , drosi-b4qvg5 , drosi-b4qvg6 , drosi-b4qzn2 , drosi-b4qzn3 , drosi-b4qzn5 , drosi-b4qzn7 , drosi-b4qzn8 , drosi-b4qzp2 , drosi-b4qzp3 , drosi-b4qzp4 , drosi-b4qzp5 , drosi-b4qzp6 , drosi-b4qzp7 , drosi-b4r1a4 , drosi-b4r025 , drosi-b4r207 , drosi-b4r662 , drosi-este6 , drosi-q670k8 , drovi-ACHE , drovi-b4lev2 , drovi-b4lf33 , drovi-b4lf51 , drovi-b4lg54 , drovi-b4lg72 , drovi-b4lgc6 , drovi-b4lgd5 , drovi-b4lgg0 , drovi-b4lgk5 , drovi-b4lgn2 , drovi-b4lh17 , drovi-b4lh18 , drovi-b4lk43 , drovi-b4ll59 , drovi-b4ll60 , drovi-b4llm5 , drovi-b4lln3 , drovi-b4lmk4 , drovi-b4lmp0 , drovi-b4lnr4 , drovi-b4lp47 , drovi-b4lpd0 , drovi-b4lps0 , drovi-b4lqc6 , drovi-b4lr00 , drovi-b4lrp6 , drovi-b4lrw2 , drovi-b4lse7 , drovi-b4lse9 , drovi-b4lsf0 , drovi-b4lsn0 , drovi-b4lsq5 , drovi-b4lt32 , drovi-b4ltr1 , drovi-b4lui7 , drovi-b4lui9 , drovi-b4luj8 , drovi-b4luk0 , drovi-b4luk3 , drovi-b4luk8 , drovi-b4luk9 , drovi-b4lul0 , drovi-b4lve2 , drovi-b4lxi9 , drovi-b4lxj8 , drovi-b4lyf3 , drovi-b4lyq2 , drovi-b4lyq3 , drovi-b4lz07 , drovi-b4lz13 , drovi-b4lz14 , drovi-b4lz15 , drovi-b4m0j7 , drovi-b4m0s0 , drovi-b4m2b6 , drovi-b4m4h7 , drovi-b4m4h8 , drovi-b4m4i0 , drovi-b4m4i2 , drovi-b4m4i3.A , drovi-b4m4i3.B , drovi-b4m4i4 , drovi-b4m4i5 , drovi-b4m4i6 , drovi-b4m4i7 , drovi-b4m4i8 , drovi-b4m4i9 , drovi-b4m4j2 , drovi-b4m5a0 , drovi-b4m5a1 , drovi-b4m5a2 , drovi-b4m6b9 , drovi-b4m7k9 , drovi-b4m9g9 , drovi-b4m9h0 , drovi-b4m564 , drovi-b4m599 , drovi-b4m918 , drovi-b4mb87 , drovi-b4mc71 , drovi-b4mfa4 , drowi-ACHE , drowi-b4mjb9 , drowi-b4mkt7 , drowi-b4mlc1 , drowi-b4mp68 , drowi-b4mqe9 , drowi-b4mqf0.2 , drowi-b4mqf1 , drowi-b4mqf3 , drowi-b4mqf4 , drowi-b4mqf5 , drowi-b4mqq6 , drowi-b4mrd1 , drowi-b4mrk3 , drowi-b4mtl5 , drowi-b4mug2 , drowi-b4muj8 , drowi-b4mv18 , drowi-b4mw32 , drowi-b4mw85 , drowi-b4mwp2 , drowi-b4mwp6 , drowi-b4mwq5 , drowi-b4mwr0 , drowi-b4mwr8 , drowi-b4mwr9 , drowi-b4mwt1 , drowi-b4mwz7 , drowi-b4mxn5 , drowi-b4my54 , drowi-b4myg1 , drowi-b4myh5 , drowi-b4n0d4 , drowi-b4n1a7 , drowi-b4n1c8 , drowi-b4n3s9 , drowi-b4n3x7 , drowi-b4n4x9 , drowi-b4n4y0 , drowi-b4n6m1 , drowi-b4n6n0 , drowi-b4n6n7 , drowi-b4n6u6 , drowi-b4n7s6 , drowi-b4n7s7 , drowi-b4n7s8 , drowi-b4n899.1 , drowi-b4n8a1 , drowi-b4n8a2 , drowi-b4n8a3 , drowi-b4n8a4 , drowi-b4n8a9 , drowi-b4n023 , drowi-b4n075 , drowi-b4n543 , drowi-b4n888 , drowi-b4n889 , drowi-b4n891 , drowi-b4n893 , drowi-b4n895 , drowi-b4n897 , drowi-b4n898 , drowi-b4n899.2 , drowi-b4nae3 , drowi-b4ner8 , drowi-b4ng76 , drowi-b4nga7 , drowi-b4ngb5 , drowi-b4nhz9 , drowi-b4nj18 , drowi-b4nj19 , drowi-b4nja7 , drowi-b4nja8 , drowi-b4nja9 , drowi-b4njk8 , drowi-b4nkc8 , drowi-b4nky0 , drowi-b4nl36 , drowi-b4nm27 , drowi-b4nn59 , drowi-b4nnc1 , drowi-b4nng1 , drowi-b4nng2 , droya-ACHE , droya-aes04 , droya-b4itg2 , droya-b4itg6 , droya-b4itu9 , droya-b4iuv4 , droya-b4iuv5 , droya-b4nxe6 , droya-b4nxg5 , droya-b4nxg6 , droya-b4nxg8 , droya-b4nxw4 , droya-b4ny57 , droya-b4ny58 , droya-b4ny86 , droya-b4nzz8 , droya-b4p0b5 , droya-b4p0q9 , droya-b4p0r0 , droya-b4p0r7 , droya-b4p0r8 , droya-b4p0r9 , droya-b4p0s0 , droya-b4p0s2 , droya-b4p0t0 , droya-b4p0t1 , droya-b4p3h4 , droya-b4p3x8 , droya-b4p5g8 , droya-b4p6c9 , droya-b4p6l9 , droya-b4p6r1 , droya-b4p6r2 , droya-b4p7u4 , droya-b4p8w7 , droya-b4p023 , droya-b4p241 , droya-b4p774 , droya-b4pat9 , droya-b4pbl1 , droya-b4pd22 , droya-b4pd70 , droya-b4pdm8 , droya-b4pet9 , droya-b4pff9 , droya-b4pga7 , droya-b4pgu0 , droya-b4pig3 , droya-b4pjt8 , droya-b4pka2 , droya-b4plh2 , droya-b4pma3 , droya-b4pmv3 , droya-b4pmv4 , droya-b4pmv5 , droya-b4pn92 , droya-b4pp65 , droya-b4ppc5 , droya-b4ppc6 , droya-b4ppc7 , droya-b4ppc8 , droya-b4pq03 , droya-b4prg6B , droya-b4prg9 , droya-b4prh3 , droya-b4prh4 , droya-b4prh6 , droya-b4prh7 , droya-b4psz8 , droya-b4psz9 , droya-b4pv22 , droya-b4q0g5 , droya-b4q246 , droya-EST6 , droya-q71d76 , drowi-b4n7m9 , drope-b4gkk1 , droer-b3n5s3 , drose-b4i1w5 , drowi-a0a0q9x0t3 , drogr-b4jvm7 , dromo-b4ku70 , drovi-b4mcn9 , drovi-b4lty2 , drogr-b4jdu1 , drovi-a0a0q9wiq8 , dromo-b4kf70 , drosi-b2zi86 , droya-b4p2y4 , drose-b2zic5 , droer-b3n895

Title : The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization - Cuomo_2007_Science_317_1400
Author(s) : Cuomo CA , Guldener U , Xu JR , Trail F , Turgeon BG , Di Pietro A , Walton JD , Ma LJ , Baker SE , Rep M , Adam G , Antoniw J , Baldwin T , Calvo S , Chang YL , Decaprio D , Gale LR , Gnerre S , Goswami RS , Hammond-Kosack K , Harris LJ , Hilburn K , Kennell JC , Kroken S , Magnuson JK , Mannhaupt G , Mauceli E , Mewes HW , Mitterbauer R , Muehlbauer G , Munsterkotter M , Nelson D , O'Donnell K , Ouellet T , Qi W , Quesneville H , Roncero MI , Seong KY , Tetko IV , Urban M , Waalwijk C , Ward TJ , Yao J , Birren BW , Kistler HC
Ref : Science , 317 :1400 , 2007
Abstract : We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.
ESTHER : Cuomo_2007_Science_317_1400
PubMedSearch : Cuomo_2007_Science_317_1400
PubMedID: 17823352
Gene_locus related to this paper: fusof-f9fxz4 , gibze-a8w610 , gibze-b1pdn0 , gibze-i1r9e6 , gibze-i1rda9 , gibze-i1rdk7 , gibze-i1rec8 , gibze-i1rgs0 , gibze-i1rgy0 , gibze-i1rh52 , gibze-i1rhi8 , gibze-i1rig9 , gibze-i1rip5 , gibze-i1rpg6 , gibze-i1rsg2 , gibze-i1rv36 , gibze-i1rxm5 , gibze-i1rxp8 , gibze-i1rxv5 , gibze-i1s1u3 , gibze-i1s3j9 , gibze-i1s6l7 , gibze-i1s8i8 , gibze-i1s9x4 , gibze-ppme1 , gibze-q4huy1 , gibze-i1rg17 , gibze-i1rb76 , gibze-i1s1m7 , gibze-i1s3z6 , gibze-i1rd78 , gibze-i1rgl9 , gibze-i1rjp7 , gibze-i1s1q6 , gibze-i1ri35 , gibze-i1rf76 , gibze-i1rhp3 , gibza-a0a016pda4 , gibza-a0a016pl96 , gibze-i1rjb5 , gibze-i1rkc4 , gibze-a0a1c3ylb1 , gibze-gra11 , gibze-fsl2

Title : Genome sequence of Aedes aegypti, a major arbovirus vector - Nene_2007_Science_316_1718
Author(s) : Nene V , Wortman JR , Lawson D , Haas B , Kodira C , Tu ZJ , Loftus B , Xi Z , Megy K , Grabherr M , Ren Q , Zdobnov EM , Lobo NF , Campbell KS , Brown SE , Bonaldo MF , Zhu J , Sinkins SP , Hogenkamp DG , Amedeo P , Arensburger P , Atkinson PW , Bidwell S , Biedler J , Birney E , Bruggner RV , Costas J , Coy MR , Crabtree J , Crawford M , Debruyn B , Decaprio D , Eiglmeier K , Eisenstadt E , El-Dorry H , Gelbart WM , Gomes SL , Hammond M , Hannick LI , Hogan JR , Holmes MH , Jaffe D , Johnston JS , Kennedy RC , Koo H , Kravitz S , Kriventseva EV , Kulp D , LaButti K , Lee E , Li S , Lovin DD , Mao C , Mauceli E , Menck CF , Miller JR , Montgomery P , Mori A , Nascimento AL , Naveira HF , Nusbaum C , O'Leary S , Orvis J , Pertea M , Quesneville H , Reidenbach KR , Rogers YH , Roth CW , Schneider JR , Schatz M , Shumway M , Stanke M , Stinson EO , Tubio JM , Vanzee JP , Verjovski-Almeida S , Werner D , White O , Wyder S , Zeng Q , Zhao Q , Zhao Y , Hill CA , Raikhel AS , Soares MB , Knudson DL , Lee NH , Galagan J , Salzberg SL , Paulsen IT , Dimopoulos G , Collins FH , Birren B , Fraser-Liggett CM , Severson DW
Ref : Science , 316 :1718 , 2007
Abstract : We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
ESTHER : Nene_2007_Science_316_1718
PubMedSearch : Nene_2007_Science_316_1718
PubMedID: 17510324
Gene_locus related to this paper: aedae-ACHE , aedae-ACHE1 , aedae-glita , aedae-q0iea6 , aedae-q0iev6 , aedae-q0ifn6 , aedae-q0ifn8 , aedae-q0ifn9 , aedae-q0ifp0 , aedae-q0ig41 , aedae-q1dgl0 , aedae-q1dh03 , aedae-q1dh19 , aedae-q1hqe6 , aedae-Q8ITU8 , aedae-Q8MMJ6 , aedae-Q8T9V6 , aedae-q16e91 , aedae-q16f04 , aedae-q16f25 , aedae-q16f26 , aedae-q16f28 , aedae-q16f29 , aedae-q16f30 , aedae-q16gq5 , aedae-q16iq5 , aedae-q16je0 , aedae-q16je1 , aedae-q16je2 , aedae-q16ks8 , aedae-q16lf2 , aedae-q16lv6 , aedae-q16m61 , aedae-q16mc1 , aedae-q16mc6 , aedae-q16mc7 , aedae-q16md1 , aedae-q16ms7 , aedae-q16nk5 , aedae-q16rl5 , aedae-q16rz9 , aedae-q16si8 , aedae-q16t49 , aedae-q16wf1 , aedae-q16x18 , aedae-q16xp8 , aedae-q16xu6 , aedae-q16xw5 , aedae-q16xw6 , aedae-q16y04 , aedae-q16y05 , aedae-q16y06 , aedae-q16y07 , aedae-q16y39 , aedae-q16y40 , aedae-q16yg4 , aedae-q16z03 , aedae-q17aa7 , aedae-q17av1 , aedae-q17av2 , aedae-q17av3 , aedae-q17av4 , aedae-q17b28 , aedae-q17b29 , aedae-q17b30 , aedae-q17b31 , aedae-q17b32 , aedae-q17bm3 , aedae-q17bm4 , aedae-q17bv7 , aedae-q17c44 , aedae-q17cz1 , aedae-q17d32 , aedae-q17g39 , aedae-q17g40 , aedae-q17g41 , aedae-q17g42 , aedae-q17g43 , aedae-q17g44 , aedae-q17gb8 , aedae-q17gr3 , aedae-q17if7 , aedae-q17if9 , aedae-q17ig1 , aedae-q17ig2 , aedae-q17is4 , aedae-q17l09 , aedae-q17m26 , aedae-q17mg9 , aedae-q17mv4 , aedae-q17mv5 , aedae-q17mv6 , aedae-q17mv7 , aedae-q17mw8 , aedae-q17mw9 , aedae-q17nw5 , aedae-q17nx5 , aedae-q17pa4 , aedae-q17q69 , aedae-q170k7 , aedae-q171y4 , aedae-q172e0 , aedae-q176i8 , aedae-q176j0 , aedae-q177k1 , aedae-q177k2 , aedae-q177l9 , aedae-j9hic3 , aedae-q179r9 , aedae-u483 , aedae-j9hj23 , aedae-q17d68 , aedae-q177c7 , aedae-q0ifp1 , aedae-a0a1s4fx83 , aedae-a0a1s4g2m0 , aedae-q1hr49

Title : Combined evidence annotation of transposable elements in genome sequences - Quesneville_2005_PLoS.Comput.Biol_1_166
Author(s) : Quesneville H , Bergman CM , Andrieu O , Autard D , Nouaud D , Ashburner M , Anxolabehere D
Ref : PLoS Comput Biol , 1 :166 , 2005
Abstract : Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila.
ESTHER : Quesneville_2005_PLoS.Comput.Biol_1_166
PubMedSearch : Quesneville_2005_PLoS.Comput.Biol_1_166
PubMedID: 16110336
Gene_locus related to this paper: drome-CG9542 , drome-CG11309 , drome-KRAKEN , drome-nrtac

Title : Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation - Eiglmeier_2005_Insect.Biochem.Mol.Biol_35_799
Author(s) : Eiglmeier K , Wincker P , Cattolico L , Anthouard V , Holm I , Eckenberg R , Quesneville H , Jaillon O , Collins FH , Weissenbach J , Brey PT , Roth CW
Ref : Insect Biochemistry & Molecular Biology , 35 :799 , 2005
Abstract : The only natural mechanism of malaria transmission in sub-Saharan Africa is the mosquito, generally Anopheles gambiae. Blocking malaria parasite transmission by stopping the development of Plasmodium in the insect vector would provide a useful alternative to the current methods of malaria control. Toward this end, it is important to understand the molecular basis of the malaria parasite refractory phenotype in An. gambiae mosquito strains. We have selected and sequenced six bacterial artificial chromosome (BAC) clones from the Pen-1 region that is the major quantitative trait locus involved in Plasmodium encapsulation. The sequence and the annotation of five overlapping BAC clones plus one adjacent, but not contiguous clone, totaling 585kb of genomic sequence from the centromeric end of the Pen-1 region of the PEST strain were compared to that of the genome sequence of the same strain produced by the whole genome shotgun technique. This project identified 23 putative mosquito genes plus putative copies of the retrotransposable elements BEL12 and TRANSIBN1_AG in the six BAC clones. Nineteen of the predicted genes are most similar to their Drosophila melanogaster homologs while one is more closely related to vertebrate genes. Comparison of these new BAC sequences plus previously published BAC sequences to the cognate region of the assembled genome sequence identified three retrotransposons present in one sequence version but not the other. One of these elements, Indy, has not been previously described. These observations provide evidence for the recent active transposition of these elements and demonstrate the plasticity of the Anopheles genome. The BAC sequences strongly support the public whole genome shotgun assembly and automatic annotation while also demonstrating the benefit of complementary genome sequences and of human curation. Importantly, the data demonstrate the differences in the genome sequence of an individual mosquito compared to that of a hypothetical, average genome sequence generated by whole genome shotgun assembly.
ESTHER : Eiglmeier_2005_Insect.Biochem.Mol.Biol_35_799
PubMedSearch : Eiglmeier_2005_Insect.Biochem.Mol.Biol_35_799
PubMedID: 15944077
Gene_locus related to this paper: anoga-agCG50851 , anoga-ebiG8504